Strain identifier

BacDive ID: 6049

Type strain: Yes

Species: Halomonas denitrificans

Strain Designation: M29

Strain history: CIP <- 2008, DSMZ <- K.K. Kim, KAIST, Daejon, Korea: strain M29

NCBI tax ID(s): 370769 (species)

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General

@ref: 7266

BacDive-ID: 6049

DSM-Number: 18045

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Halomonas denitrificans M29 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from solar saltern.

NCBI tax id

  • NCBI tax id: 370769
  • Matching level: species

strain history

@refhistory
7266<- K. K. Kim
118897CIP <- 2008, DSMZ <- K.K. Kim, KAIST, Daejon, Korea: strain M29

doi: 10.13145/bacdive6049.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Oceanospirillales
  • family: Halomonadaceae
  • genus: Halomonas
  • species: Halomonas denitrificans
  • full scientific name: Halomonas denitrificans Kim et al. 2007

@ref: 7266

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Halomonadaceae

genus: Halomonas

species: Halomonas denitrificans

full scientific name: Halomonas denitrificans Kim et al. 2007

strain designation: M29

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31987negative1.2-1.6 µm0.6-0.8 µmrod-shapedyes
118897negativerod-shapedyes

pigmentation

  • @ref: 31987
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7266BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514; with strain-specific modifications) Composition: NaCl 80.0 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
7266R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
36923Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
118897CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13
118897CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
7266positivegrowth28mesophilic
31987positivegrowth05-50
31987positiveoptimum25-35mesophilic
36923positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31987positivegrowth07-10alkaliphile
31987positiveoptimum08-09

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31987aerobe
118897facultative anaerobe

spore formation

  • @ref: 31987
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31987NaClpositivegrowth02-20 %
31987NaClpositiveoptimum08-10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
31987370543-hydroxybutyrate+carbon source
3198730089acetate+carbon source
3198716449alanine+carbon source
3198716947citrate+carbon source
3198724996lactate+carbon source
3198725115malate+carbon source
3198715792malonate+carbon source
3198726271proline+carbon source
3198717272propionate+carbon source
3198717822serine+carbon source
3198731011valerate+carbon source
3198717632nitrate+reduction
11889717632nitrate+reduction
11889716301nitrite-reduction

metabolite production

  • @ref: 118897
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31987catalase+1.11.1.6
31987cytochrome oxidase+1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
118897oxidase+
118897catalase+1.11.1.6
118897urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118897-+---+----++--------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
7266solar salternRepublic of KoreaKORAsia
118897Environment, Solar salternRepublic of KoreaKORAsiaAnmyeondo

isolation source categories

  • Cat1: #Condition
  • Cat2: #Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_63832.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_48;96_430;97_996;98_20284;99_63832&stattab=map
  • Last taxonomy: Halomonas
  • 16S sequence: AM229317
  • Sequence Identity:
  • Total samples: 2290
  • soil counts: 68
  • aquatic counts: 505
  • animal counts: 1696
  • plant counts: 21

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
72661Risk group (German classification)
1188971Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Halomonas denitrificans genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 1089AB3672301089ena370769
31987Halomonas denitrificans partial 16S rRNA gene, type strain M29TAM2293171489nuccore370769

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halomonas denitrificans DSM 18045GCA_003056305contigncbi370769
66792Halomonas denitrificans strain DSM 18045370769.4wgspatric370769

GC content

  • @ref: 31987
  • GC-content: 53.8-55.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno98.928yes
anaerobicno96.9yes
halophileyes94.028yes
spore-formingno96.919yes
glucose-utilyes86.033no
aerobicyes82.739no
flagellatedyes66.833no
thermophileno98.398yes
motileyes91.58no
glucose-fermentno77.297no

External links

@ref: 7266

culture collection no.: DSM 18045, CIP 109894, KCTC 12665

straininfo link

  • @ref: 75536
  • straininfo: 302755

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17392185Halomonas gomseomensis sp. nov., Halomonas janggokensis sp. nov., Halomonas salaria sp. nov. and Halomonas denitrificans sp. nov., moderately halophilic bacteria isolated from saline water.Kim KK, Jin L, Yang HC, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.64767-02007DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Halomonas/*classification/genetics/isolation & purification/physiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sodium Chloride, *Water MicrobiologyGenetics
Phylogeny24425813Halomonas huangheensis sp. nov., a moderately halophilic bacterium isolated from a saline-alkali soil.Miao C, Jia F, Wan Y, Zhang W, Lin M, Jin WInt J Syst Evol Microbiol10.1099/ijs.0.056556-02013Alkalies, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Halomonas/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salinity, *Soil Microbiology, Ubiquinone/chemistryGenetics
Metabolism26495103Biodegradation of Para Amino Acetanilide by Halomonas sp. TBZ3.Hajizadeh N, Sefidi Heris Y, Zununi Vahed S, Vallipour J, Hejazi MA, Golabi SM, Asadpour-Zeynali K, Hejazi MSJundishapur J Microbiol10.5812/jjm.186222015

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
7266Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18045)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18045
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
31987Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128241
36923Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7689
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
75536Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID302755.1StrainInfo: A central database for resolving microbial strain identifiers
118897Curators of the CIPCollection of Institut Pasteur (CIP 109894)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109894